I might try pinning down the quilt too if you're getting this significant of a pucker. I get a teensy pucker from the mild stretching that happens when you attach the binding to the front of the quilt - but usually it's so small that when I fold over the binding it's invisible and you cannot feel it so I don't worry about it. Somewhere the binding is stretching even if you don't realize it...I would suspect it's in an area where the weight of the quilt is pulling on the binding even though your hands are not. Maybe next time also take a moment to look at your surroundings and the table you're laying it on and the weight distribution of the quilt when you apply the binding.
It's always the smallest thing that throws us off!